December 24, 2015

Merry Christmas! The stream of microbiome research papers never appears to take a break, so I will keep on posting during the holidays. Today I found two nice review papers on the oral microbiome and cystic fibrosis microbiome, an upcoming hands-on workshop on mothur (Microbial Ecology software), the acne microbiome, and bacterial exchange in your washing machine.

Events

Throughout the year, Pat offers 4-5 workshops on mothur and programming in R for microbial ecologists. February mothur workshop by Patrick Schloss, February 8-10, Detroit

General microbiome

Review: Tools for the Microbiome: Nano and Beyond – Julie S. Biteen – ACS Nano

Human skin microbiome

Microorganisms inhabiting follicular contents of facial acne are not only Propionibacterium but also Malassezia spp. – Narifumi Akaza – The Journal of Dermatology

Human oral microbiome

ReviewBeyond the oral microbiome – Howard F. Jenkinson – Environmental Microbiology

Prevalence of Candida albicans and Candida dubliniensis in caries-free and caries-active children in relation to the oral microbiota—a clinical study – A. Al-Ahmad – Clinical Oral Investigations

Human respiratory microbiome

Looking beyond respiratory cultures: Microbiome-cytokine signatures of bacterial pneumonia and tracheobronchitis in lung transplant recipients – Jyoti Shankar – American Journal of Transplantation

The Lung Immune Response to Bacteria in Chronic Obstructive Pulmonary Disease – Paul T. King – American Journal of Respiratory and Critical Care Medicine

Review: The Microbiome in Cystic Fibrosis – Yvonne J. Huang – Clinics in Chest Medicine

Human gut microbiome

Not a very novel insight: Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing – Ravi Ranjan – Biochemical and Biophysical Research Communications

Review: The Gastrointestinal Microbiome: Alcohol Effects on the Composition of Intestinal Microbiota – Phillip A. Engen – Alcohol Research Current Reviews

Review: The First Line of Defense: The Effects of Alcohol on Post-Burn Intestinal Barrier, Immune Cells, and Microbiome – Adam M. Hammer

Microbiome models

Intestinal Microbiota Signatures Associated with Inflammation History in Mice Experiencing Recurring Colitis – David Berry – Frontiers in Microbiology

The Anti-Oxidant Drug Tempol Promotes Functional Metabolic Changes in the Gut Microbiota – Jingwei Cai – Journal of Proteome Research

Effects of the dietary protein level on the microbial composition and metabolomic profile in the hindgut of the pig – Liping Zhou – Anaerobe

Development of gut inflammation in mice colonized with mucosa-associated bacteria from patients with ulcerative colitis – Zhengyu Du – Gut Pathogens

Animal microbiome

The Metabolically Active Bacterial Microbiome of Tonsils and Mandibular Lymph Nodes of Slaughter Pigs – Evelyne Mann – Frontiers in Microbiology

Microbial community of Pacific abalone (Haliotis discus hannai) juveniles during a disease outbreak in South China – Liu-yang Shi – Aquaculture Research

The Role of Tissue-specific Microbiota in Initial Establishment Success of Pacific oysters – Ana Lokmer – Environmental Microbiology

Plant, root, and soil microbiomes

Impact of forest management practices on soil bacterial diversity and consequences for soil processes – Federica Colombo – Soil Biology and Biochemistry

Metagenomics study of endophytic bacteria in Aloe vera using next-generation technology – Mushafau Adewale Akinsanya – Genomics Data

Shifts of microbial community structure in soils of a photovoltaic plant observed using tag-encoded pyrosequencing of 16S rRNA – Shijin Wu – Applied Microbiology and Biotechnology

Copper pollution decreases the resistance of soil microbial community to subsequent dry–rewetting disturbance – Jing Li – Journal of Environmental Sciences

Switchgrass rhizospheres stimulate microbial biomass but deplete microbial necromass in agricultural soils of the upper Midwest, USA – Chao Liang – Soil Biology and Biochemistry

Water and waste microbiome

Occurrence and persistence of antibiotic resistance genes in river biofilms after wastewater inputs in small rivers – Lorenzo Proia – Environmental Pollution

Biogeochemical importance of the bacterial community in uranium waste deposited at Key Lake, Northern Saskatchewan – VF Bondici – Geomicrobiology Journal

Built environment microbiome

Bacterial Exchange in Household Washing Machines – Chris Callewaert- Frontiers in Microbiology

Survival of Antarctic Cryptoendolithic Fungi in Simulated Martian Conditions On Board the International Space Station – Onofri Silvano – Astrobiology

Darkening on lead-based pigments: Microbiological contribution – Tânia Rosado – Color Research & Application

Microbes in the news

Giant Balls of Bacteria Pile Up on Arctic Lake Beds, Ooze Toxin – Emily Benson – EOS

This Squid Could Help Humans Repel Dangerous Flesh-Eating Bacteria – Esther Inglis-Arkell – Gizmodo

Lackner Investigates Whether Brain Changes Affect Gut Microbiome – University of Buffalo

Science, publishing, and career

2015 London Naturejobs Career Expo: Science communication videos – Julie Gould – Nature Blogs
How to deal with the media
How to get a job
How to deal with articles that misrepresent science
Do you need a PhD?

Korean prosecutors seek jail time for professors in massive plagiarism scheme – Mark Zastrow – Retraction Watch

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